I’m a little nervous about this one, Gilles. It’s doing a lot more than just addressing the immediate issue, and I’m concerned about any potential side-effects that we don’t fully unocver prior to release.
I’d suggest a two-pronged approach: 1. use my alternative method for 1.10.1 to solve the immediate issue. It only affects this one, rather unusual, corner-case that was reported here. So the impact can be easily contained and won’t impact anything else. 2. push your proposed solution to the master where it can soak for awhile and give us a chance to fully discover the secondary effects. Removing the unused and “not-allowed” cpus from the topology means a substantial scrub of the code base in a number of places, and your patch doesn’t really get them all. It’s going to take time to ensure everything is working correctly again. HTH Ralph > On Oct 7, 2015, at 4:29 AM, Gilles Gouaillardet > <gilles.gouaillar...@gmail.com> wrote: > > Jeff, > > there are quite a lot of changes, I did not update master yet (need extra > pairs of eyes to review this...) > so unless you want to make rc2 today and rc3 a week later, it is imho way > safer to wait for v1.10.2 > > Ralph, > any thoughts ? > > Cheers, > > Gilles > > On Wednesday, October 7, 2015, Jeff Squyres (jsquyres) <jsquy...@cisco.com > <mailto:jsquy...@cisco.com>> wrote: > Is this something that needs to go into v1.10.1? > > If so, a PR needs to be filed ASAP. We were supposed to make the next 1.10.1 > RC yesterday, but slipped to today due to some last second patches. > > > > On Oct 7, 2015, at 4:32 AM, Gilles Gouaillardet <gil...@rist.or.jp > > <javascript:;>> wrote: > > > > Marcin, > > > > here is a patch for the master, hopefully it fixes all the issues we > > discussed > > i will make sure it applies fine vs latest 1.10 tarball from tomorrow > > > > Cheers, > > > > Gilles > > > > > > On 10/6/2015 7:22 PM, marcin.krotkiewski wrote: > >> Gilles, > >> > >> Yes, it seemed that all was fine with binding in the patched 1.10.1rc1 - > >> thank you. Eagerly waiting for the other patches, let me know and I will > >> test them later this week. > >> > >> Marcin > >> > >> > >> > >> On 10/06/2015 12:09 PM, Gilles Gouaillardet wrote: > >>> Marcin, > >>> > >>> my understanding is that in this case, patched v1.10.1rc1 is working just > >>> fine. > >>> am I right ? > >>> > >>> I prepared two patches > >>> one to remove the warning when binding on one core if only one core is > >>> available, > >>> an other one to add a warning if the user asks a binding policy that > >>> makes no sense with the required mapping policy > >>> > >>> I will finalize them tomorrow hopefully > >>> > >>> Cheers, > >>> > >>> Gilles > >>> > >>> On Tuesday, October 6, 2015, marcin.krotkiewski > >>> <marcin.krotkiew...@gmail.com <javascript:;>> wrote: > >>> Hi, Gilles > >>>> you mentionned you had one failure with 1.10.1rc1 and -bind-to core > >>>> could you please send the full details (script, allocation and output) > >>>> in your slurm script, you can do > >>>> srun -N $SLURM_NNODES -n $SLURM_NNODES --cpu_bind=none -l grep > >>>> Cpus_allowed_list /proc/self/status > >>>> before invoking mpirun > >>>> > >>> It was an interactive job allocated with > >>> > >>> salloc --account=staff --ntasks=32 --mem-per-cpu=2G --time=120:0:0 > >>> > >>> The slurm environment is the following > >>> > >>> SLURM_JOBID=12714491 > >>> SLURM_JOB_CPUS_PER_NODE='4,2,5(x2),4,7,5' > >>> SLURM_JOB_ID=12714491 > >>> SLURM_JOB_NODELIST='c1-[2,4,8,13,16,23,26]' > >>> SLURM_JOB_NUM_NODES=7 > >>> SLURM_JOB_PARTITION=normal > >>> SLURM_MEM_PER_CPU=2048 > >>> SLURM_NNODES=7 > >>> SLURM_NODELIST='c1-[2,4,8,13,16,23,26]' > >>> SLURM_NODE_ALIASES='(null)' > >>> SLURM_NPROCS=32 > >>> SLURM_NTASKS=32 > >>> SLURM_SUBMIT_DIR=/cluster/home/marcink > >>> SLURM_SUBMIT_HOST=login-0-1.local > >>> SLURM_TASKS_PER_NODE='4,2,5(x2),4,7,5' > >>> > >>> The output of the command you asked for is > >>> > >>> 0: c1-2.local Cpus_allowed_list: 1-4,17-20 > >>> 1: c1-4.local Cpus_allowed_list: 1,15,17,31 > >>> 2: c1-8.local Cpus_allowed_list: 0,5,9,13-14,16,21,25,29-30 > >>> 3: c1-13.local Cpus_allowed_list: 3-7,19-23 > >>> 4: c1-16.local Cpus_allowed_list: 12-15,28-31 > >>> 5: c1-23.local Cpus_allowed_list: 2-4,8,13-15,18-20,24,29-31 > >>> 6: c1-26.local Cpus_allowed_list: 1,6,11,13,15,17,22,27,29,31 > >>> > >>> Running with command > >>> > >>> mpirun --mca rmaps_base_verbose 10 --hetero-nodes --bind-to core > >>> --report-bindings --map-by socket -np 32 ./affinity > >>> > >>> I have attached two output files: one for the original 1.10.1rc1, one for > >>> the patched version. > >>> > >>> When I said 'failed in one case' I was not precise. I got an error on > >>> node c1-8, which was the first one to have different number of MPI > >>> processes on the two sockets. It would also fail on some later nodes, > >>> just that because of the error we never got there. > >>> > >>> Let me know if you need more. > >>> > >>> Marcin > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>>> Cheers, > >>>> > >>>> Gilles > >>>> > >>>> On 10/4/2015 11:55 PM, marcin.krotkiewski wrote: > >>>>> Hi, all, > >>>>> > >>>>> I played a bit more and it seems that the problem results from > >>>>> > >>>>> trg_obj = opal_hwloc_base_find_min_bound_target_under_obj() > >>>>> > >>>>> called in rmaps_base_binding.c / bind_downwards being wrong. I do not > >>>>> know the reason, but I think I know when the problem happens (at least > >>>>> on 1.10.1rc1). It seems that by default openmpi maps by socket. The > >>>>> error happens when for a given compute node there is a different number > >>>>> of cores used on each socket. Consider previously studied case (the > >>>>> debug outputs I sent in last post). c1-8, which was source of error, > >>>>> has 5 mpi processes assigned, and the cpuset is the following: > >>>>> > >>>>> 0, 5, 9, 13, 14, 16, 21, 25, 29, 30 > >>>>> > >>>>> Cores 0,5 are on socket 0, cores 9, 13, 14 are on socket 1. Binding > >>>>> progresses correctly up to and including core 13 (see end of file > >>>>> out.1.10.1rc2, before the error). That is 2 cores on socket 0, and 2 > >>>>> cores on socket 1. Error is thrown when core 14 should be bound - extra > >>>>> core on socket 1 with no corresponding core on socket 0. At that point > >>>>> the returned trg_obj points to the first core on the node (os_index 0, > >>>>> socket 0). > >>>>> > >>>>> I have submitted a few other jobs and I always had an error in such > >>>>> situation. Moreover, if I now use --map-by core instead of socket, the > >>>>> error is gone, and I get my expected binding: > >>>>> > >>>>> rank 0 @ compute-1-2.local 1, 17, > >>>>> rank 1 @ compute-1-2.local 2, 18, > >>>>> rank 2 @ compute-1-2.local 3, 19, > >>>>> rank 3 @ compute-1-2.local 4, 20, > >>>>> rank 4 @ compute-1-4.local 1, 17, > >>>>> rank 5 @ compute-1-4.local 15, 31, > >>>>> rank 6 @ compute-1-8.local 0, 16, > >>>>> rank 7 @ compute-1-8.local 5, 21, > >>>>> rank 8 @ compute-1-8.local 9, 25, > >>>>> rank 9 @ compute-1-8.local 13, 29, > >>>>> rank 10 @ compute-1-8.local 14, 30, > >>>>> rank 11 @ compute-1-13.local 3, 19, > >>>>> rank 12 @ compute-1-13.local 4, 20, > >>>>> rank 13 @ compute-1-13.local 5, 21, > >>>>> rank 14 @ compute-1-13.local 6, 22, > >>>>> rank 15 @ compute-1-13.local 7, 23, > >>>>> rank 16 @ compute-1-16.local 12, 28, > >>>>> rank 17 @ compute-1-16.local 13, 29, > >>>>> rank 18 @ compute-1-16.local 14, 30, > >>>>> rank 19 @ compute-1-16.local 15, 31, > >>>>> rank 20 @ compute-1-23.local 2, 18, > >>>>> rank 29 @ compute-1-26.local 11, 27, > >>>>> rank 21 @ compute-1-23.local 3, 19, > >>>>> rank 30 @ compute-1-26.local 13, 29, > >>>>> rank 22 @ compute-1-23.local 4, 20, > >>>>> rank 31 @ compute-1-26.local 15, 31, > >>>>> rank 23 @ compute-1-23.local 8, 24, > >>>>> rank 27 @ compute-1-26.local 1, 17, > >>>>> rank 24 @ compute-1-23.local 13, 29, > >>>>> rank 28 @ compute-1-26.local 6, 22, > >>>>> rank 25 @ compute-1-23.local 14, 30, > >>>>> rank 26 @ compute-1-23.local 15, 31, > >>>>> > >>>>> Using --map-by core seems to fix the issue on 1.8.8, 1.10.0 and > >>>>> 1.10.1rc1. However, there is still a difference in behavior between > >>>>> 1.10.1rc1 and earlier versions. In the SLURM job described in last > >>>>> post, 1.10.1rc1 fails to bind only in 1 case, while the earlier > >>>>> versions fail in 21 out of 32 cases. You mentioned there was a bug in > >>>>> hwloc. Not sure if it can explain the difference in behavior. > >>>>> > >>>>> Hope this helps to nail this down. > >>>>> > >>>>> Marcin > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> On 10/04/2015 09:55 AM, Gilles Gouaillardet wrote: > >>>>>> Ralph, > >>>>>> > >>>>>> I suspect ompi tries to bind to threads outside the cpuset. > >>>>>> this could be pretty similar to a previous issue when ompi tried to > >>>>>> bind to cores outside the cpuset. > >>>>>> /* when a core has more than one thread, would ompi assume all the > >>>>>> threads are available if the core is available ? */ > >>>>>> I will investigate this from tomorrow > >>>>>> > >>>>>> Cheers, > >>>>>> > >>>>>> Gilles > >>>>>> > >>>>>> On Sunday, October 4, 2015, Ralph Castain <r...@open-mpi.org > >>>>>> <javascript:;>> wrote: > >>>>>> Thanks - please go ahead and release that allocation as I’m not going > >>>>>> to get to this immediately. I’ve got several hot irons in the fire > >>>>>> right now, and I’m not sure when I’ll get a chance to track this down. > >>>>>> > >>>>>> Gilles or anyone else who might have time - feel free to take a gander > >>>>>> and see if something pops out at you. > >>>>>> > >>>>>> Ralph > >>>>>> > >>>>>> > >>>>>>> On Oct 3, 2015, at 11:05 AM, marcin.krotkiewski > >>>>>>> <marcin.krotkiew...@gmail.com <javascript:;>> wrote: > >>>>>>> > >>>>>>> > >>>>>>> Done. I have compiled 1.10.0 and 1.10.rc1 with --enable-debug and > >>>>>>> executed > >>>>>>> > >>>>>>> mpirun --mca rmaps_base_verbose 10 --hetero-nodes --report-bindings > >>>>>>> --bind-to core -np 32 ./affinity > >>>>>>> > >>>>>>> In case of 1.10.rc1 I have also added :overload-allowed - output in a > >>>>>>> separate file. This option did not make much difference for 1.10.0, > >>>>>>> so I did not attach it here. > >>>>>>> > >>>>>>> First thing I noted for 1.10.0 are lines like > >>>>>>> > >>>>>>> [login-0-1.local:03399] [[37945,0],0] GOT 1 CPUS > >>>>>>> [login-0-1.local:03399] [[37945,0],0] PROC [[37945,1],27] BITMAP > >>>>>>> [login-0-1.local:03399] [[37945,0],0] PROC [[37945,1],27] ON c1-26 IS > >>>>>>> NOT BOUND > >>>>>>> > >>>>>>> with an empty BITMAP. > >>>>>>> > >>>>>>> The SLURM environment is > >>>>>>> > >>>>>>> set | grep SLURM > >>>>>>> SLURM_JOBID=12714491 > >>>>>>> SLURM_JOB_CPUS_PER_NODE='4,2,5(x2),4,7,5' > >>>>>>> SLURM_JOB_ID=12714491 > >>>>>>> SLURM_JOB_NODELIST='c1-[2,4,8,13,16,23,26]' > >>>>>>> SLURM_JOB_NUM_NODES=7 > >>>>>>> SLURM_JOB_PARTITION=normal > >>>>>>> SLURM_MEM_PER_CPU=2048 > >>>>>>> SLURM_NNODES=7 > >>>>>>> SLURM_NODELIST='c1-[2,4,8,13,16,23,26]' > >>>>>>> SLURM_NODE_ALIASES='(null)' > >>>>>>> SLURM_NPROCS=32 > >>>>>>> SLURM_NTASKS=32 > >>>>>>> SLURM_SUBMIT_DIR=/cluster/home/marcink > >>>>>>> SLURM_SUBMIT_HOST=login-0-1.local > >>>>>>> SLURM_TASKS_PER_NODE='4,2,5(x2),4,7,5' > >>>>>>> > >>>>>>> I have submitted an interactive job on screen for 120 hours now to > >>>>>>> work with one example, and not change it for every post :) > >>>>>>> > >>>>>>> If you need anything else, let me know. I could introduce some > >>>>>>> patch/printfs and recompile, if you need it. > >>>>>>> > >>>>>>> Marcin > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> On 10/03/2015 07:17 PM, Ralph Castain wrote: > >>>>>>>> Rats - just realized I have no way to test this as none of the > >>>>>>>> machines I can access are setup for cgroup-based multi-tenant. Is > >>>>>>>> this a debug version of OMPI? If not, can you rebuild OMPI with > >>>>>>>> —enable-debug? > >>>>>>>> > >>>>>>>> Then please run it with —mca rmaps_base_verbose 10 and pass along > >>>>>>>> the output. > >>>>>>>> > >>>>>>>> Thanks > >>>>>>>> Ralph > >>>>>>>> > >>>>>>>> > >>>>>>>>> On Oct 3, 2015, at 10:09 AM, Ralph Castain <r...@open-mpi.org > >>>>>>>>> <javascript:;>> wrote: > >>>>>>>>> > >>>>>>>>> What version of slurm is this? I might try to debug it here. I’m > >>>>>>>>> not sure where the problem lies just yet. > >>>>>>>>> > >>>>>>>>> > >>>>>>>>>> On Oct 3, 2015, at 8:59 AM, marcin.krotkiewski > >>>>>>>>>> <marcin.krotkiew...@gmail.com <javascript:;>> wrote: > >>>>>>>>>> > >>>>>>>>>> Here is the output of lstopo. In short, (0,16) are core 0, (1,17) > >>>>>>>>>> - core 1 etc. > >>>>>>>>>> > >>>>>>>>>> Machine (64GB) > >>>>>>>>>> NUMANode L#0 (P#0 32GB) > >>>>>>>>>> Socket L#0 + L3 L#0 (20MB) > >>>>>>>>>> L2 L#0 (256KB) + L1d L#0 (32KB) + L1i L#0 (32KB) + Core L#0 > >>>>>>>>>> PU L#0 (P#0) > >>>>>>>>>> PU L#1 (P#16) > >>>>>>>>>> L2 L#1 (256KB) + L1d L#1 (32KB) + L1i L#1 (32KB) + Core L#1 > >>>>>>>>>> PU L#2 (P#1) > >>>>>>>>>> PU L#3 (P#17) > >>>>>>>>>> L2 L#2 (256KB) + L1d L#2 (32KB) + L1i L#2 (32KB) + Core L#2 > >>>>>>>>>> PU L#4 (P#2) > >>>>>>>>>> PU L#5 (P#18) > >>>>>>>>>> L2 L#3 (256KB) + L1d L#3 (32KB) + L1i L#3 (32KB) + Core L#3 > >>>>>>>>>> PU L#6 (P#3) > >>>>>>>>>> PU L#7 (P#19) > >>>>>>>>>> L2 L#4 (256KB) + L1d L#4 (32KB) + L1i L#4 (32KB) + Core L#4 > >>>>>>>>>> PU L#8 (P#4) > >>>>>>>>>> PU L#9 (P#20) > >>>>>>>>>> L2 L#5 (256KB) + L1d L#5 (32KB) + L1i L#5 (32KB) + Core L#5 > >>>>>>>>>> PU L#10 (P#5) > >>>>>>>>>> PU L#11 (P#21) > >>>>>>>>>> L2 L#6 (256KB) + L1d L#6 (32KB) + L1i L#6 (32KB) + Core L#6 > >>>>>>>>>> PU L#12 (P#6) > >>>>>>>>>> PU L#13 (P#22) > >>>>>>>>>> L2 L#7 (256KB) + L1d L#7 (32KB) + L1i L#7 (32KB) + Core L#7 > >>>>>>>>>> PU L#14 (P#7) > >>>>>>>>>> PU L#15 (P#23) > >>>>>>>>>> HostBridge L#0 > >>>>>>>>>> PCIBridge > >>>>>>>>>> PCI 8086:1521 > >>>>>>>>>> Net L#0 "eth0" > >>>>>>>>>> PCI 8086:1521 > >>>>>>>>>> Net L#1 "eth1" > >>>>>>>>>> PCIBridge > >>>>>>>>>> PCI 15b3:1003 > >>>>>>>>>> Net L#2 "ib0" > >>>>>>>>>> OpenFabrics L#3 "mlx4_0" > >>>>>>>>>> PCIBridge > >>>>>>>>>> PCI 102b:0532 > >>>>>>>>>> PCI 8086:1d02 > >>>>>>>>>> Block L#4 "sda" > >>>>>>>>>> NUMANode L#1 (P#1 32GB) + Socket L#1 + L3 L#1 (20MB) > >>>>>>>>>> L2 L#8 (256KB) + L1d L#8 (32KB) + L1i L#8 (32KB) + Core L#8 > >>>>>>>>>> PU L#16 (P#8) > >>>>>>>>>> PU L#17 (P#24) > >>>>>>>>>> L2 L#9 (256KB) + L1d L#9 (32KB) + L1i L#9 (32KB) + Core L#9 > >>>>>>>>>> PU L#18 (P#9) > >>>>>>>>>> PU L#19 (P#25) > >>>>>>>>>> L2 L#10 (256KB) + L1d L#10 (32KB) + L1i L#10 (32KB) + Core L#10 > >>>>>>>>>> PU L#20 (P#10) > >>>>>>>>>> PU L#21 (P#26) > >>>>>>>>>> L2 L#11 (256KB) + L1d L#11 (32KB) + L1i L#11 (32KB) + Core L#11 > >>>>>>>>>> PU L#22 (P#11) > >>>>>>>>>> PU L#23 (P#27) > >>>>>>>>>> L2 L#12 (256KB) + L1d L#12 (32KB) + L1i L#12 (32KB) + Core L#12 > >>>>>>>>>> PU L#24 (P#12) > >>>>>>>>>> PU L#25 (P#28) > >>>>>>>>>> L2 L#13 (256KB) + L1d L#13 (32KB) + L1i L#13 (32KB) + Core L#13 > >>>>>>>>>> PU L#26 (P#13) > >>>>>>>>>> PU L#27 (P#29) > >>>>>>>>>> L2 L#14 (256KB) + L1d L#14 (32KB) + L1i L#14 (32KB) + Core L#14 > >>>>>>>>>> PU L#28 (P#14) > >>>>>>>>>> PU L#29 (P#30) > >>>>>>>>>> L2 L#15 (256KB) + L1d L#15 (32KB) + L1i L#15 (32KB) + Core L#15 > >>>>>>>>>> PU L#30 (P#15) > >>>>>>>>>> PU L#31 (P#31) > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> On 10/03/2015 05:46 PM, Ralph Castain wrote: > >>>>>>>>>>> Maybe I’m just misreading your HT map - that slurm nodelist > >>>>>>>>>>> syntax is a new one to me, but they tend to change things around. > >>>>>>>>>>> Could you run lstopo on one of those compute nodes and send the > >>>>>>>>>>> output? > >>>>>>>>>>> > >>>>>>>>>>> I’m just suspicious because I’m not seeing a clear pairing of HT > >>>>>>>>>>> numbers in your output, but HT numbering is BIOS-specific and I > >>>>>>>>>>> may just not be understanding your particular pattern. Our error > >>>>>>>>>>> message is clearly indicating that we are seeing individual HTs > >>>>>>>>>>> (and not complete cores) assigned, and I don’t know the source of > >>>>>>>>>>> that confusion. > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>>> On Oct 3, 2015, at 8:28 AM, marcin.krotkiewski > >>>>>>>>>>>> <marcin.krotkiew...@gmail.com <javascript:;>> wrote: > >>>>>>>>>>>> > >>>>>>>>>>>> > >>>>>>>>>>>> On 10/03/2015 04:38 PM, Ralph Castain wrote: > >>>>>>>>>>>>> If mpirun isn’t trying to do any binding, then you will of > >>>>>>>>>>>>> course get the right mapping as we’ll just inherit whatever we > >>>>>>>>>>>>> received. > >>>>>>>>>>>> Yes. I meant that whatever you received (what SLURM gives) is a > >>>>>>>>>>>> correct cpu map and assigns _whole_ CPUs, not a single HT to MPI > >>>>>>>>>>>> processes. In the case mentioned earlier openmpi should start 6 > >>>>>>>>>>>> tasks on c1-30. If HT would be treated as separate and > >>>>>>>>>>>> independent cores, sched_getaffinity of an MPI process started > >>>>>>>>>>>> on c1-30 would return a map with 6 entries only. In my case it > >>>>>>>>>>>> returns a map > >>>>>>>>>>>> with 12 entries - 2 for each core. So one process is in > >>>>>>>>>>>> fact allocated both HTs, not only one. Is what I'm saying > >>>>>>>>>>>> correct? > >>>>>>>>>>>> > >>>>>>>>>>>>> Looking at your output, it’s pretty clear that you are getting > >>>>>>>>>>>>> independent HTs assigned and not full cores. > >>>>>>>>>>>> How do you mean? Is the above understanding wrong? I would > >>>>>>>>>>>> expect that on c1-30 with --bind-to core openmpi should bind to > >>>>>>>>>>>> logical cores 0 and 16 (rank 0), 1 and 17 (rank 2) and so on. > >>>>>>>>>>>> All those logical cores are available in sched_getaffinity map, > >>>>>>>>>>>> and there is twice as many logical cores as there are MPI > >>>>>>>>>>>> processes started on the node. > >>>>>>>>>>>> > >>>>>>>>>>>>> My guess is that something in slurm has changed such that it > >>>>>>>>>>>>> detects that HT has been enabled, and then begins treating the > >>>>>>>>>>>>> HTs as completely independent cpus. > >>>>>>>>>>>>> > >>>>>>>>>>>>> Try changing “-bind-to core” to “-bind-to hwthread > >>>>>>>>>>>>> -use-hwthread-cpus” and see if that works > >>>>>>>>>>>>> > >>>>>>>>>>>> I have and the binding is wrong. For example, I got this output > >>>>>>>>>>>> > >>>>>>>>>>>> rank 0 @ compute-1-30.local 0, > >>>>>>>>>>>> rank 1 @ compute-1-30.local 16, > >>>>>>>>>>>> > >>>>>>>>>>>> Which means that two ranks have been bound to the same physical > >>>>>>>>>>>> core (logical cores 0 and 16 are two HTs of the same core). If I > >>>>>>>>>>>> use --bind-to core, I get the following correct binding > >>>>>>>>>>>> > >>>>>>>>>>>> rank 0 @ compute-1-30.local 0, 16, > >>>>>>>>>>>> > >>>>>>>>>>>> The problem is many other ranks get bad binding with 'rank XXX > >>>>>>>>>>>> is not bound (or bound to all available processors)' warning. > >>>>>>>>>>>> > >>>>>>>>>>>> But I think I was not entirely correct saying that 1.10.1rc1 did > >>>>>>>>>>>> not fix things. It still might have improved something, but not > >>>>>>>>>>>> everything. Consider this job: > >>>>>>>>>>>> > >>>>>>>>>>>> SLURM_JOB_CPUS_PER_NODE='5,4,6,5(x2),7,5,9,5,7,6' > >>>>>>>>>>>> SLURM_JOB_NODELIST='c8-[31,34],c9-[30-32,35-36],c10-[31-34]' > >>>>>>>>>>>> > >>>>>>>>>>>> If I run 32 tasks as follows (with 1.10.1rc1) > >>>>>>>>>>>> > >>>>>>>>>>>> mpirun --hetero-nodes --report-bindings --bind-to core -np 32 > >>>>>>>>>>>> ./affinity > >>>>>>>>>>>> > >>>>>>>>>>>> I get the following error: > >>>>>>>>>>>> > >>>>>>>>>>>> -------------------------------------------------------------------------- > >>>>>>>>>>>> A request was made to bind to that would result in binding more > >>>>>>>>>>>> processes than cpus on a resource: > >>>>>>>>>>>> > >>>>>>>>>>>> Bind to: CORE > >>>>>>>>>>>> Node: c9-31 > >>>>>>>>>>>> #processes: 2 > >>>>>>>>>>>> #cpus: 1 > >>>>>>>>>>>> > >>>>>>>>>>>> You can override this protection by adding the "overload-allowed" > >>>>>>>>>>>> option to your binding directive. > >>>>>>>>>>>> -------------------------------------------------------------------------- > >>>>>>>>>>>> > >>>>>>>>>>>> > >>>>>>>>>>>> If I now use --bind-to core:overload-allowed, then openmpi > >>>>>>>>>>>> starts and _most_ of the threads are bound correctly (i.e., map > >>>>>>>>>>>> contains two logical cores in ALL cases), except this case that > >>>>>>>>>>>> required the overload flag: > >>>>>>>>>>>> > >>>>>>>>>>>> rank 15 @ compute-9-31.local 1, 17, > >>>>>>>>>>>> rank 16 @ compute-9-31.local 11, 27, > >>>>>>>>>>>> rank 17 @ compute-9-31.local 2, 18, > >>>>>>>>>>>> rank 18 @ compute-9-31.local 12, 28, > >>>>>>>>>>>> rank 19 @ compute-9-31.local 1, 17, > >>>>>>>>>>>> > >>>>>>>>>>>> Note pair 1,17 is used twice. The original SLURM delivered map > >>>>>>>>>>>> (no binding) on this node is > >>>>>>>>>>>> > >>>>>>>>>>>> rank 15 @ compute-9-31.local 1, 2, 11, 12, 13, 17, 18, 27, 28, > >>>>>>>>>>>> 29, > >>>>>>>>>>>> rank 16 @ compute-9-31.local 1, 2, 11, 12, 13, 17, 18, 27, 28, > >>>>>>>>>>>> 29, > >>>>>>>>>>>> rank 17 @ compute-9-31.local 1, 2, 11, 12, 13, 17, 18, 27, 28, > >>>>>>>>>>>> 29, > >>>>>>>>>>>> rank 18 @ compute-9-31.local 1, 2, 11, 12, 13, 17, 18, 27, 28, > >>>>>>>>>>>> 29, > >>>>>>>>>>>> rank 19 @ compute-9-31.local 1, 2, 11, 12, 13, 17, 18, 27, 28, > >>>>>>>>>>>> 29, > >>>>>>>>>>>> > >>>>>>>>>>>> Why does openmpi use cores (1,17) twice instead of using core > >>>>>>>>>>>> (13,29)? Clearly, the original SLURM-delivered map has 5 CPUs > >>>>>>>>>>>> included, enough for 5 MPI processes. > >>>>>>>>>>>> > >>>>>>>>>>>> Cheers, > >>>>>>>>>>>> > >>>>>>>>>>>> Marcin > >>>>>>>>>>>> > >>>>>>>>>>>> > >>>>>>>>>>>>> > >>>>>>>>>>>>>> On Oct 3, 2015, at 7:12 AM, marcin.krotkiewski > >>>>>>>>>>>>>> <marcin.krotkiew...@gmail.com <javascript:;>> wrote: > >>>>>>>>>>>>>> > >>>>>>>>>>>>>> > >>>>>>>>>>>>>> On 10/03/2015 01:06 PM, Ralph Castain wrote: > >>>>>>>>>>>>>>> Thanks Marcin. Looking at this, I’m guessing that Slurm may > >>>>>>>>>>>>>>> be treating HTs as “cores” - i.e., as independent cpus. Any > >>>>>>>>>>>>>>> chance that is true? > >>>>>>>>>>>>>> Not to the best of my knowledge, and at least not > >>>>>>>>>>>>>> intentionally. SLURM starts as many processes as there are > >>>>>>>>>>>>>> physical cores, not threads. To verify this, consider this > >>>>>>>>>>>>>> test case: > >>>>>> > >>>>>> > >>>>>> _______________________________________________ > >>>>>> users mailing list > >>>>>> > >>>>>> us...@open-mpi.org <javascript:;> > >>>>>> > >>>>>> Subscription: > >>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users > >>>>>> <http://www.open-mpi.org/mailman/listinfo.cgi/users> > >>>>>> > >>>>>> Link to this post: > >>>>>> http://www.open-mpi.org/community/lists/users/2015/10/27790.php > >>>>>> <http://www.open-mpi.org/community/lists/users/2015/10/27790.php> > >>>>> > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> users mailing list > >>>>> > >>>>> us...@open-mpi.org <javascript:;> > >>>>> > >>>>> Subscription: > >>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users > >>>>> <http://www.open-mpi.org/mailman/listinfo.cgi/users> > >>>>> > >>>>> Link to this post: > >>>>> http://www.open-mpi.org/community/lists/users/2015/10/27791.php > >>>>> <http://www.open-mpi.org/community/lists/users/2015/10/27791.php> > >>>> > >>>> > >>>> > >>>> _______________________________________________ > >>>> users mailing list > >>>> > >>>> us...@open-mpi.org <javascript:;> > >>>> > >>>> Subscription: > >>>> http://www.open-mpi.org/mailman/listinfo.cgi/users > >>>> <http://www.open-mpi.org/mailman/listinfo.cgi/users> > >>>> > >>>> Link to this post: > >>>> http://www.open-mpi.org/community/lists/users/2015/10/27792.php > >>>> <http://www.open-mpi.org/community/lists/users/2015/10/27792.php> > >>> > >>> > >>> > >>> _______________________________________________ > >>> users mailing list > >>> > >>> us...@open-mpi.org <javascript:;> > >>> > >>> Subscription: > >>> http://www.open-mpi.org/mailman/listinfo.cgi/users > >>> <http://www.open-mpi.org/mailman/listinfo.cgi/users> > >>> > >>> Link to this post: > >>> http://www.open-mpi.org/community/lists/users/2015/10/27814.php > >>> <http://www.open-mpi.org/community/lists/users/2015/10/27814.php> > >> > >> > >> > >> _______________________________________________ > >> users mailing list > >> > >> us...@open-mpi.org <javascript:;> > >> > >> Subscription: > >> http://www.open-mpi.org/mailman/listinfo.cgi/users > >> <http://www.open-mpi.org/mailman/listinfo.cgi/users> > >> > >> Link to this post: > >> http://www.open-mpi.org/community/lists/users/2015/10/27815.php > >> <http://www.open-mpi.org/community/lists/users/2015/10/27815.php> > > > > <heterogeneous_topologies.patch>_______________________________________________ > > users mailing list > > us...@open-mpi.org <javascript:;> > > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > > <http://www.open-mpi.org/mailman/listinfo.cgi/users> > > Link to this post: > > http://www.open-mpi.org/community/lists/users/2015/10/27827.php > > <http://www.open-mpi.org/community/lists/users/2015/10/27827.php> > > > -- > Jeff Squyres > jsquy...@cisco.com <javascript:;> > For corporate legal information go to: > http://www.cisco.com/web/about/doing_business/legal/cri/ > <http://www.cisco.com/web/about/doing_business/legal/cri/> > > _______________________________________________ > users mailing list > us...@open-mpi.org <javascript:;> > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > <http://www.open-mpi.org/mailman/listinfo.cgi/users> > Link to this post: > http://www.open-mpi.org/community/lists/users/2015/10/27828.php > <http://www.open-mpi.org/community/lists/users/2015/10/27828.php> > _______________________________________________ > users mailing list > us...@open-mpi.org > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > Link to this post: > http://www.open-mpi.org/community/lists/users/2015/10/27830.php
